rs147459127
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001349253.2(SCN11A):c.4077G>A(p.Val1359Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000361 in 1,606,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001349253.2 synonymous
Scores
Clinical Significance
Conservation
Publications
- autosomal dominant hereditary sensory and autonomic neuropathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- familial episodic pain syndrome with predominantly lower limb involvementInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
- hereditary sensory and autonomic neuropathy type 7Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
- sodium channelopathy-related small fiber neuropathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCN11A | NM_001349253.2 | c.4077G>A | p.Val1359Val | synonymous_variant | Exon 29 of 30 | ENST00000302328.9 | NP_001336182.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152060Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000813 AC: 20AN: 245922 AF XY: 0.0000678 show subpopulations
GnomAD4 exome AF: 0.0000357 AC: 52AN: 1454832Hom.: 0 Cov.: 30 AF XY: 0.0000360 AC XY: 26AN XY: 722780 show subpopulations
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152060Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74274 show subpopulations
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Hereditary sensory and autonomic neuropathy type 7;C3809899:Familial episodic pain syndrome with predominantly lower limb involvement Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at